Multiple sequence alignment - TraesCS5D01G261500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G261500 chr5D 100.000 4318 0 0 1 4318 367811257 367815574 0.000000e+00 7974.0
1 TraesCS5D01G261500 chr5D 87.037 1242 153 7 998 2235 367991259 367992496 0.000000e+00 1395.0
2 TraesCS5D01G261500 chr5D 85.898 1319 167 11 932 2245 367981176 367982480 0.000000e+00 1387.0
3 TraesCS5D01G261500 chr5D 86.865 1241 157 4 998 2235 367996697 367997934 0.000000e+00 1384.0
4 TraesCS5D01G261500 chr5D 85.000 100 9 1 2920 3019 367995347 367995440 3.550000e-16 97.1
5 TraesCS5D01G261500 chr5A 94.420 1595 54 14 2358 3943 469922928 469924496 0.000000e+00 2420.0
6 TraesCS5D01G261500 chr5A 91.672 1597 96 14 714 2292 469906050 469907627 0.000000e+00 2178.0
7 TraesCS5D01G261500 chr5A 88.795 1544 146 15 713 2246 469898604 469900130 0.000000e+00 1868.0
8 TraesCS5D01G261500 chr5A 86.785 1241 158 4 998 2235 470038802 470040039 0.000000e+00 1378.0
9 TraesCS5D01G261500 chr5A 90.705 624 32 13 111 715 469897948 469898564 0.000000e+00 808.0
10 TraesCS5D01G261500 chr5A 86.885 610 35 12 111 706 469905427 469906005 3.640000e-180 641.0
11 TraesCS5D01G261500 chr5A 97.276 257 6 1 4022 4278 469924494 469924749 6.630000e-118 435.0
12 TraesCS5D01G261500 chr5A 92.683 123 8 1 1 122 95560576 95560454 4.440000e-40 176.0
13 TraesCS5D01G261500 chr5A 89.922 129 11 2 1 129 368971737 368971611 9.610000e-37 165.0
14 TraesCS5D01G261500 chr5A 98.077 52 1 0 2290 2341 469922880 469922931 1.650000e-14 91.6
15 TraesCS5D01G261500 chr5B 88.387 1550 146 17 713 2246 435770327 435771858 0.000000e+00 1834.0
16 TraesCS5D01G261500 chr5B 86.202 1319 169 10 932 2245 435943013 435944323 0.000000e+00 1415.0
17 TraesCS5D01G261500 chr5B 86.140 1241 166 5 998 2235 435949615 435950852 0.000000e+00 1334.0
18 TraesCS5D01G261500 chr5B 91.102 472 32 6 252 715 435769819 435770288 7.880000e-177 630.0
19 TraesCS5D01G261500 chr5B 96.396 111 4 0 1 111 695946683 695946793 2.650000e-42 183.0
20 TraesCS5D01G261500 chr5B 87.000 100 13 0 2920 3019 436070834 436070933 3.530000e-21 113.0
21 TraesCS5D01G261500 chr5B 82.645 121 15 2 3233 3353 435947040 435947154 7.640000e-18 102.0
22 TraesCS5D01G261500 chr3A 93.548 124 5 3 1 122 138545527 138545405 9.540000e-42 182.0
23 TraesCS5D01G261500 chr6A 95.495 111 5 0 1 111 127525636 127525526 1.230000e-40 178.0
24 TraesCS5D01G261500 chr6A 95.495 111 5 0 1 111 181277241 181277131 1.230000e-40 178.0
25 TraesCS5D01G261500 chr6A 95.495 111 5 0 1 111 541001356 541001246 1.230000e-40 178.0
26 TraesCS5D01G261500 chr6A 91.304 92 6 1 3941 4030 190660435 190660344 1.630000e-24 124.0
27 TraesCS5D01G261500 chr6A 91.304 92 6 1 3941 4030 190738358 190738267 1.630000e-24 124.0
28 TraesCS5D01G261500 chr2A 95.495 111 5 0 1 111 73918651 73918761 1.230000e-40 178.0
29 TraesCS5D01G261500 chr1A 95.495 111 5 0 1 111 219298680 219298790 1.230000e-40 178.0
30 TraesCS5D01G261500 chr1A 91.304 92 6 1 3940 4029 209362156 209362065 1.630000e-24 124.0
31 TraesCS5D01G261500 chr7A 91.489 94 4 3 3941 4030 726995713 726995620 4.530000e-25 126.0
32 TraesCS5D01G261500 chr7A 94.937 79 2 1 3948 4024 581850986 581850908 5.860000e-24 122.0
33 TraesCS5D01G261500 chr7D 91.209 91 6 1 3939 4027 412001468 412001378 5.860000e-24 122.0
34 TraesCS5D01G261500 chr6B 89.109 101 7 3 3940 4037 713833554 713833455 5.860000e-24 122.0
35 TraesCS5D01G261500 chr6D 91.954 87 5 1 3940 4024 199210414 199210328 2.110000e-23 121.0
36 TraesCS5D01G261500 chr3D 90.426 94 5 3 3941 4032 66523464 66523373 2.110000e-23 121.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G261500 chr5D 367811257 367815574 4317 False 7974.000000 7974 100.000000 1 4318 1 chr5D.!!$F1 4317
1 TraesCS5D01G261500 chr5D 367981176 367982480 1304 False 1387.000000 1387 85.898000 932 2245 1 chr5D.!!$F2 1313
2 TraesCS5D01G261500 chr5D 367991259 367997934 6675 False 958.700000 1395 86.300667 998 3019 3 chr5D.!!$F3 2021
3 TraesCS5D01G261500 chr5A 469905427 469907627 2200 False 1409.500000 2178 89.278500 111 2292 2 chr5A.!!$F3 2181
4 TraesCS5D01G261500 chr5A 470038802 470040039 1237 False 1378.000000 1378 86.785000 998 2235 1 chr5A.!!$F1 1237
5 TraesCS5D01G261500 chr5A 469897948 469900130 2182 False 1338.000000 1868 89.750000 111 2246 2 chr5A.!!$F2 2135
6 TraesCS5D01G261500 chr5A 469922880 469924749 1869 False 982.200000 2420 96.591000 2290 4278 3 chr5A.!!$F4 1988
7 TraesCS5D01G261500 chr5B 435769819 435771858 2039 False 1232.000000 1834 89.744500 252 2246 2 chr5B.!!$F3 1994
8 TraesCS5D01G261500 chr5B 435943013 435950852 7839 False 950.333333 1415 84.995667 932 3353 3 chr5B.!!$F4 2421

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
410 432 0.248621 GCGGCGGGAAATCATTTCAG 60.249 55.0 12.27 6.48 41.43 3.02 F
446 468 0.855598 CTCCCATCCCAATCCCATGT 59.144 55.0 0.00 0.00 0.00 3.21 F
605 635 0.953960 CTTGCCGTGGTTGAGGTACC 60.954 60.0 2.73 2.73 38.73 3.34 F
2032 7589 0.386352 CACACAACTTGGCAGCGATG 60.386 55.0 0.00 0.00 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1649 0.322997 TGTCTTTATTGTGGGGGCGG 60.323 55.000 0.0 0.0 0.00 6.13 R
1922 2035 0.595095 GCTCCACCTTTGTTGCTCTG 59.405 55.000 0.0 0.0 0.00 3.35 R
2497 14596 3.067320 GGAATTACCTGATCTGCAAAGGC 59.933 47.826 0.0 0.0 34.18 4.35 R
3804 15911 0.532862 CAGAACACAAGGACGCCAGT 60.533 55.000 0.0 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.787601 CTGTGTTGCAGCATGTTCTT 57.212 45.000 6.50 0.00 38.52 2.52
27 28 2.658285 CTGTGTTGCAGCATGTTCTTC 58.342 47.619 6.50 0.00 38.52 2.87
28 29 2.022934 TGTGTTGCAGCATGTTCTTCA 58.977 42.857 6.50 0.00 39.31 3.02
29 30 2.624364 TGTGTTGCAGCATGTTCTTCAT 59.376 40.909 6.50 0.00 39.31 2.57
30 31 3.819902 TGTGTTGCAGCATGTTCTTCATA 59.180 39.130 6.50 0.00 39.31 2.15
31 32 4.083164 TGTGTTGCAGCATGTTCTTCATAG 60.083 41.667 6.50 0.00 39.31 2.23
32 33 4.074259 TGTTGCAGCATGTTCTTCATAGT 58.926 39.130 0.00 0.00 39.31 2.12
33 34 4.083164 TGTTGCAGCATGTTCTTCATAGTG 60.083 41.667 0.00 0.00 39.31 2.74
34 35 3.941573 TGCAGCATGTTCTTCATAGTGA 58.058 40.909 0.00 0.00 39.31 3.41
35 36 4.325972 TGCAGCATGTTCTTCATAGTGAA 58.674 39.130 0.00 0.00 39.31 3.18
36 37 4.945543 TGCAGCATGTTCTTCATAGTGAAT 59.054 37.500 0.00 0.00 35.23 2.57
37 38 5.065602 TGCAGCATGTTCTTCATAGTGAATC 59.934 40.000 0.00 0.00 35.23 2.52
38 39 5.505324 GCAGCATGTTCTTCATAGTGAATCC 60.505 44.000 0.00 0.00 35.23 3.01
39 40 4.813161 AGCATGTTCTTCATAGTGAATCCG 59.187 41.667 0.00 0.00 35.59 4.18
40 41 4.024556 GCATGTTCTTCATAGTGAATCCGG 60.025 45.833 0.00 0.00 35.59 5.14
41 42 4.819105 TGTTCTTCATAGTGAATCCGGT 57.181 40.909 0.00 0.00 35.59 5.28
42 43 4.503910 TGTTCTTCATAGTGAATCCGGTG 58.496 43.478 0.00 0.00 35.59 4.94
43 44 3.179443 TCTTCATAGTGAATCCGGTGC 57.821 47.619 0.00 0.00 35.59 5.01
44 45 2.766263 TCTTCATAGTGAATCCGGTGCT 59.234 45.455 0.00 0.00 35.59 4.40
45 46 2.602257 TCATAGTGAATCCGGTGCTG 57.398 50.000 0.00 0.00 0.00 4.41
46 47 1.831106 TCATAGTGAATCCGGTGCTGT 59.169 47.619 0.00 0.00 0.00 4.40
47 48 1.935873 CATAGTGAATCCGGTGCTGTG 59.064 52.381 0.00 0.00 0.00 3.66
48 49 0.249120 TAGTGAATCCGGTGCTGTGG 59.751 55.000 0.00 0.00 0.00 4.17
49 50 1.003839 GTGAATCCGGTGCTGTGGA 60.004 57.895 0.00 0.00 38.95 4.02
50 51 0.605319 GTGAATCCGGTGCTGTGGAA 60.605 55.000 0.00 0.00 37.90 3.53
51 52 0.327924 TGAATCCGGTGCTGTGGAAT 59.672 50.000 0.00 0.00 37.90 3.01
52 53 1.557371 TGAATCCGGTGCTGTGGAATA 59.443 47.619 0.00 0.00 37.90 1.75
53 54 2.172505 TGAATCCGGTGCTGTGGAATAT 59.827 45.455 0.00 0.00 37.90 1.28
54 55 3.214328 GAATCCGGTGCTGTGGAATATT 58.786 45.455 0.00 0.00 37.90 1.28
55 56 4.141597 TGAATCCGGTGCTGTGGAATATTA 60.142 41.667 0.00 0.00 37.90 0.98
56 57 4.640771 ATCCGGTGCTGTGGAATATTAT 57.359 40.909 0.00 0.00 37.90 1.28
57 58 3.738982 TCCGGTGCTGTGGAATATTATG 58.261 45.455 0.00 0.00 0.00 1.90
58 59 2.226437 CCGGTGCTGTGGAATATTATGC 59.774 50.000 0.00 0.00 0.00 3.14
59 60 3.141398 CGGTGCTGTGGAATATTATGCT 58.859 45.455 0.00 0.00 0.00 3.79
60 61 3.565482 CGGTGCTGTGGAATATTATGCTT 59.435 43.478 0.00 0.00 0.00 3.91
61 62 4.555313 CGGTGCTGTGGAATATTATGCTTG 60.555 45.833 0.00 0.00 0.00 4.01
62 63 4.293415 GTGCTGTGGAATATTATGCTTGC 58.707 43.478 0.00 0.00 0.00 4.01
63 64 3.952967 TGCTGTGGAATATTATGCTTGCA 59.047 39.130 0.00 0.00 0.00 4.08
64 65 4.585581 TGCTGTGGAATATTATGCTTGCAT 59.414 37.500 12.88 12.88 0.00 3.96
65 66 5.769162 TGCTGTGGAATATTATGCTTGCATA 59.231 36.000 10.84 10.84 0.00 3.14
66 67 6.264970 TGCTGTGGAATATTATGCTTGCATAA 59.735 34.615 24.35 24.35 0.00 1.90
67 68 7.147312 GCTGTGGAATATTATGCTTGCATAAA 58.853 34.615 25.43 17.12 31.69 1.40
68 69 7.652909 GCTGTGGAATATTATGCTTGCATAAAA 59.347 33.333 25.43 11.51 31.69 1.52
69 70 8.870160 TGTGGAATATTATGCTTGCATAAAAC 57.130 30.769 25.43 17.72 31.69 2.43
70 71 8.473219 TGTGGAATATTATGCTTGCATAAAACA 58.527 29.630 25.43 19.31 31.69 2.83
71 72 9.480053 GTGGAATATTATGCTTGCATAAAACAT 57.520 29.630 25.43 17.60 31.69 2.71
72 73 9.695526 TGGAATATTATGCTTGCATAAAACATC 57.304 29.630 25.43 20.18 31.69 3.06
73 74 9.695526 GGAATATTATGCTTGCATAAAACATCA 57.304 29.630 25.43 7.52 31.69 3.07
81 82 7.583230 TGCTTGCATAAAACATCAATTTTTCC 58.417 30.769 0.00 0.00 33.80 3.13
82 83 7.022979 GCTTGCATAAAACATCAATTTTTCCC 58.977 34.615 0.00 0.00 33.80 3.97
83 84 6.718454 TGCATAAAACATCAATTTTTCCCG 57.282 33.333 0.00 0.00 33.80 5.14
84 85 6.226787 TGCATAAAACATCAATTTTTCCCGT 58.773 32.000 0.00 0.00 33.80 5.28
85 86 6.708054 TGCATAAAACATCAATTTTTCCCGTT 59.292 30.769 0.00 0.00 33.80 4.44
86 87 7.014702 GCATAAAACATCAATTTTTCCCGTTG 58.985 34.615 0.00 0.00 33.80 4.10
87 88 5.416862 AAAACATCAATTTTTCCCGTTGC 57.583 34.783 0.00 0.00 0.00 4.17
88 89 3.742433 ACATCAATTTTTCCCGTTGCA 57.258 38.095 0.00 0.00 0.00 4.08
89 90 4.065321 ACATCAATTTTTCCCGTTGCAA 57.935 36.364 0.00 0.00 0.00 4.08
90 91 3.807071 ACATCAATTTTTCCCGTTGCAAC 59.193 39.130 19.89 19.89 0.00 4.17
100 101 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
101 102 2.669910 TTGCAACGCACGGGCATA 60.670 55.556 11.77 0.00 38.71 3.14
102 103 2.043405 TTGCAACGCACGGGCATAT 61.043 52.632 11.77 0.00 38.71 1.78
103 104 2.024588 GCAACGCACGGGCATATG 59.975 61.111 11.77 6.17 41.24 1.78
104 105 2.760159 GCAACGCACGGGCATATGT 61.760 57.895 11.77 0.00 41.24 2.29
105 106 1.062365 CAACGCACGGGCATATGTG 59.938 57.895 11.77 0.00 41.24 3.21
141 144 3.834489 TGGAAAATGGCAAAGCTTTCA 57.166 38.095 9.23 5.84 30.89 2.69
159 162 3.423539 TCATCCAGAAAACAGGACAGG 57.576 47.619 0.00 0.00 36.60 4.00
177 180 3.871594 ACAGGCTCGAATTTTTAGATCCG 59.128 43.478 0.00 0.00 0.00 4.18
188 194 7.410407 CGAATTTTTAGATCCGCCAAAGTTTTC 60.410 37.037 0.00 0.00 0.00 2.29
193 199 4.620982 AGATCCGCCAAAGTTTTCTTTTG 58.379 39.130 0.00 0.00 46.55 2.44
194 200 4.340950 AGATCCGCCAAAGTTTTCTTTTGA 59.659 37.500 0.00 0.00 46.55 2.69
195 201 4.457834 TCCGCCAAAGTTTTCTTTTGAA 57.542 36.364 0.00 0.00 46.55 2.69
196 202 4.822026 TCCGCCAAAGTTTTCTTTTGAAA 58.178 34.783 0.00 0.00 46.55 2.69
238 247 1.719529 TTTTACCCGAGTCCAGTGGA 58.280 50.000 8.12 8.12 0.00 4.02
239 248 1.263356 TTTACCCGAGTCCAGTGGAG 58.737 55.000 13.61 2.55 29.39 3.86
240 249 0.613853 TTACCCGAGTCCAGTGGAGG 60.614 60.000 13.61 12.98 29.39 4.30
241 250 3.775654 CCCGAGTCCAGTGGAGGC 61.776 72.222 13.61 6.62 29.39 4.70
261 270 1.894466 CAGAATGGACAATGTTGGGCA 59.106 47.619 0.00 0.00 0.00 5.36
410 432 0.248621 GCGGCGGGAAATCATTTCAG 60.249 55.000 12.27 6.48 41.43 3.02
446 468 0.855598 CTCCCATCCCAATCCCATGT 59.144 55.000 0.00 0.00 0.00 3.21
503 533 3.917760 GAGTCCTCGATGCCCCCG 61.918 72.222 0.00 0.00 0.00 5.73
525 555 1.061570 GCTCGCGGAATGCTTTCTG 59.938 57.895 15.15 15.15 43.27 3.02
603 633 1.340088 TACTTGCCGTGGTTGAGGTA 58.660 50.000 0.00 0.00 0.00 3.08
605 635 0.953960 CTTGCCGTGGTTGAGGTACC 60.954 60.000 2.73 2.73 38.73 3.34
662 692 4.348754 AGGGTTTGTAGTTACTGGCTGTAA 59.651 41.667 12.29 12.29 38.67 2.41
715 745 3.071479 GCACGAGTGTTCCTTGGATTTA 58.929 45.455 5.07 0.00 0.00 1.40
749 827 4.455877 CACTTTGGGTAACTGGAGATTGTC 59.544 45.833 0.00 0.00 0.00 3.18
750 829 3.328382 TTGGGTAACTGGAGATTGTCG 57.672 47.619 0.00 0.00 0.00 4.35
751 830 2.531771 TGGGTAACTGGAGATTGTCGA 58.468 47.619 0.00 0.00 0.00 4.20
774 853 1.750193 TTTTAAGCCTGGAGATGCGG 58.250 50.000 0.00 0.00 0.00 5.69
840 927 1.967066 CCTTGGCACATTGGTTGGTAA 59.033 47.619 0.00 0.00 39.30 2.85
860 947 8.792830 TGGTAAAATAACCATGAAAGAGAGAG 57.207 34.615 0.00 0.00 44.68 3.20
903 1002 7.370383 TCATCCTCTTTCTTTGCACATAAAAC 58.630 34.615 0.00 0.00 0.00 2.43
961 1069 4.717233 TGAAATGTGTGTTTGCAGAAGT 57.283 36.364 0.00 0.00 0.00 3.01
967 1075 2.345341 GTGTGTTTGCAGAAGTGTTTGC 59.655 45.455 0.00 0.00 40.67 3.68
1040 1148 6.484308 ACCAAATCAAAGAAGCAAAGAAATGG 59.516 34.615 0.00 0.00 0.00 3.16
1062 1170 3.146066 GGAATGCATCATAAACCGCCTA 58.854 45.455 0.00 0.00 0.00 3.93
1217 1325 3.691609 CCAAGTTATGCCCTTCTGTTCTC 59.308 47.826 0.00 0.00 0.00 2.87
1220 1328 2.239907 GTTATGCCCTTCTGTTCTCCCT 59.760 50.000 0.00 0.00 0.00 4.20
1285 1393 2.496899 AATTGATGAAGCCTGGTCGT 57.503 45.000 0.00 0.00 0.00 4.34
1449 1557 2.548057 TGCGAAGAATGTGAAAGGTGAC 59.452 45.455 0.00 0.00 0.00 3.67
1452 1560 3.058914 CGAAGAATGTGAAAGGTGACCAC 60.059 47.826 3.63 0.00 0.00 4.16
1534 1647 4.402155 TCCTTGGTGATTGCATTAATGGTC 59.598 41.667 17.02 2.07 0.00 4.02
1535 1648 4.353737 CTTGGTGATTGCATTAATGGTCG 58.646 43.478 17.02 0.00 0.00 4.79
1536 1649 2.098934 TGGTGATTGCATTAATGGTCGC 59.901 45.455 17.02 3.17 0.00 5.19
1606 1719 3.313526 CGGCGATGAGAAATGGAAAGATT 59.686 43.478 0.00 0.00 0.00 2.40
1710 1823 4.039730 ACTGAAGACATGTCAGCTAACTGT 59.960 41.667 27.02 15.94 45.35 3.55
1760 1873 6.849588 ATTGGAAGAAAGTTTTGCAATGAC 57.150 33.333 0.00 2.38 42.51 3.06
1836 1949 7.124721 TCTGGATCAGAGATATAGATGGGAAG 58.875 42.308 0.00 0.00 35.39 3.46
1860 1973 6.708054 AGATATGCATAGTAACTGCTCAAACC 59.292 38.462 12.79 0.00 40.34 3.27
1865 1978 3.838244 AGTAACTGCTCAAACCAGTCA 57.162 42.857 0.00 0.00 42.37 3.41
1866 1979 3.467803 AGTAACTGCTCAAACCAGTCAC 58.532 45.455 0.00 0.00 42.37 3.67
1882 1995 3.869832 CAGTCACTATGATGCCAGAACTG 59.130 47.826 0.00 0.00 0.00 3.16
1922 2035 1.092921 TGGACACTTGACAACACGGC 61.093 55.000 0.00 0.00 0.00 5.68
1943 2059 1.856265 GAGCAACAAAGGTGGAGCCG 61.856 60.000 0.00 0.00 43.70 5.52
1968 2084 5.578157 AGTACAACATTAAGAACCCACCT 57.422 39.130 0.00 0.00 0.00 4.00
2026 2142 1.545428 GGATCCTCACACAACTTGGCA 60.545 52.381 3.84 0.00 0.00 4.92
2029 2145 1.280746 CTCACACAACTTGGCAGCG 59.719 57.895 0.00 0.00 0.00 5.18
2032 7589 0.386352 CACACAACTTGGCAGCGATG 60.386 55.000 0.00 0.00 0.00 3.84
2068 7625 5.276461 TGAGTTGCTTAGTGAGAACTTCA 57.724 39.130 0.00 0.00 30.79 3.02
2082 14178 6.800892 GTGAGAACTTCAAGATTGATTTGAGC 59.199 38.462 0.00 0.00 37.61 4.26
2114 14210 2.912956 AGCTGTTAGATTTCAGTCCCCA 59.087 45.455 0.00 0.00 34.57 4.96
2116 14212 3.262420 CTGTTAGATTTCAGTCCCCACG 58.738 50.000 0.00 0.00 0.00 4.94
2119 14218 1.749258 GATTTCAGTCCCCACGGGC 60.749 63.158 0.00 0.00 43.94 6.13
2121 14220 2.484287 ATTTCAGTCCCCACGGGCAG 62.484 60.000 0.00 0.00 43.94 4.85
2142 14241 3.004106 AGAACTTGCAATCTCACAACTGC 59.996 43.478 0.00 0.00 35.32 4.40
2148 14247 2.286950 GCAATCTCACAACTGCGTGAAA 60.287 45.455 2.65 0.00 44.97 2.69
2302 14401 7.930325 CCAGACTTTATGAAGATGAGCATAAGA 59.070 37.037 3.94 0.00 38.00 2.10
2337 14436 7.041030 TGTTGGCTGAAATCTAATTTACGTCAA 60.041 33.333 0.00 0.00 31.47 3.18
2338 14437 7.441890 TGGCTGAAATCTAATTTACGTCAAA 57.558 32.000 0.00 0.00 31.47 2.69
2339 14438 7.526608 TGGCTGAAATCTAATTTACGTCAAAG 58.473 34.615 0.00 0.00 31.47 2.77
2340 14439 7.389330 TGGCTGAAATCTAATTTACGTCAAAGA 59.611 33.333 0.00 0.00 31.47 2.52
2341 14440 8.234546 GGCTGAAATCTAATTTACGTCAAAGAA 58.765 33.333 0.00 0.00 31.47 2.52
2342 14441 9.052080 GCTGAAATCTAATTTACGTCAAAGAAC 57.948 33.333 0.00 0.00 31.47 3.01
2343 14442 9.543018 CTGAAATCTAATTTACGTCAAAGAACC 57.457 33.333 0.00 0.00 31.47 3.62
2344 14443 9.280174 TGAAATCTAATTTACGTCAAAGAACCT 57.720 29.630 0.00 0.00 31.47 3.50
2356 14455 8.617290 ACGTCAAAGAACCTTTATTATTCTGT 57.383 30.769 0.00 0.00 33.01 3.41
2463 14562 1.944032 TGGATGATGTGATGCGACAG 58.056 50.000 0.00 0.00 0.00 3.51
2464 14563 0.585357 GGATGATGTGATGCGACAGC 59.415 55.000 0.00 0.00 45.41 4.40
2497 14596 7.690637 GCATGAAAAACAATCAAATATGTGCAG 59.309 33.333 0.00 0.00 29.95 4.41
2498 14597 7.119605 TGAAAAACAATCAAATATGTGCAGC 57.880 32.000 0.00 0.00 0.00 5.25
2538 14637 9.760077 GTAATTCCTTATCGAGATGGAAGTTAA 57.240 33.333 25.88 11.68 41.20 2.01
2544 14643 8.141909 CCTTATCGAGATGGAAGTTAACATACA 58.858 37.037 8.61 2.81 0.00 2.29
2545 14644 8.867112 TTATCGAGATGGAAGTTAACATACAC 57.133 34.615 8.61 0.00 0.00 2.90
2549 14648 7.544566 TCGAGATGGAAGTTAACATACACTTTC 59.455 37.037 8.61 0.87 33.22 2.62
2647 14746 3.165071 TGTCTTACATGAGACTCCAGCA 58.835 45.455 13.87 0.00 44.99 4.41
2664 14763 3.647771 AACCAAGGTCCCTCCGGC 61.648 66.667 0.00 0.00 41.99 6.13
2712 14811 5.506317 CGGGATGAGGAAACATTATTTGCTC 60.506 44.000 12.40 12.40 44.03 4.26
2715 14814 5.295431 TGAGGAAACATTATTTGCTCGTG 57.705 39.130 13.83 0.00 45.85 4.35
2729 14828 6.621316 TTTGCTCGTGTGGAAAAGTTTATA 57.379 33.333 0.00 0.00 0.00 0.98
2835 14934 3.393089 AGTTGACTTGACTACAGGCTG 57.607 47.619 14.16 14.16 0.00 4.85
2856 14955 1.590238 CTACTCAGGCGATTGAAAGCG 59.410 52.381 0.00 0.00 41.38 4.68
2859 14958 1.019278 TCAGGCGATTGAAAGCGTCC 61.019 55.000 1.20 4.15 44.45 4.79
2944 15043 3.003480 CCGCTCTAGCTTGCTAGTTTTT 58.997 45.455 23.70 0.00 39.32 1.94
2973 15072 7.560368 ACCTGTATCAATTCTAGTTTCCTCTG 58.440 38.462 0.00 0.00 0.00 3.35
3110 15209 8.743714 TGAATCTATGCATATCTGTGTACCTAG 58.256 37.037 6.92 0.00 0.00 3.02
3166 15265 5.161943 AGTTGCCTAGTTACTGGGTTAAG 57.838 43.478 16.03 0.00 34.44 1.85
3171 15270 4.222366 GCCTAGTTACTGGGTTAAGAGTGT 59.778 45.833 16.03 0.00 34.44 3.55
3188 15287 6.901081 AGAGTGTTTTCTTTTCTAATGGGG 57.099 37.500 0.00 0.00 0.00 4.96
3205 15304 4.097017 TGGGGATTCTAGGTTTTCCCTA 57.903 45.455 15.37 9.75 46.00 3.53
3206 15305 4.652628 TGGGGATTCTAGGTTTTCCCTAT 58.347 43.478 15.37 0.00 45.00 2.57
3216 15322 9.457436 TTCTAGGTTTTCCCTATTGTATTTGAC 57.543 33.333 0.00 0.00 45.00 3.18
3217 15323 8.832735 TCTAGGTTTTCCCTATTGTATTTGACT 58.167 33.333 0.00 0.00 45.00 3.41
3262 15368 1.896220 TCAACTTCGAAAGCTGGCAT 58.104 45.000 0.00 0.00 0.00 4.40
3283 15389 2.497138 TGCTTCACAGAATCACAGTGG 58.503 47.619 0.00 0.00 36.79 4.00
3290 15396 2.740714 GAATCACAGTGGCGACGGC 61.741 63.158 15.43 15.43 38.90 5.68
3299 15405 4.891727 GGCGACGGCGATGGTGAT 62.892 66.667 18.90 0.00 41.24 3.06
3397 15504 4.263443 GCGTCTTCTTTAGTCTCGAATGAC 59.737 45.833 0.00 0.00 37.23 3.06
3401 15508 5.477291 TCTTCTTTAGTCTCGAATGACTGGT 59.523 40.000 15.53 0.00 45.70 4.00
3466 15573 4.883585 TCTGATGTTATGTTTGAGCATCCC 59.116 41.667 0.00 0.00 36.17 3.85
3489 15596 3.820557 ACCAACTATTGCCGCTATGAAT 58.179 40.909 0.00 0.00 0.00 2.57
3530 15637 0.109319 ACATTTCGCGGTGCAAATCC 60.109 50.000 6.13 0.00 0.00 3.01
3540 15647 1.269726 GGTGCAAATCCCTTGTGTGTG 60.270 52.381 0.00 0.00 37.36 3.82
3628 15735 2.995258 GAGAGCAAGTTCAGAGCTTCTG 59.005 50.000 0.00 6.79 45.59 3.02
3664 15771 4.826733 ACAAACTGTCACTATGGCATTCAA 59.173 37.500 4.78 0.00 28.30 2.69
3670 15777 3.555956 GTCACTATGGCATTCAAGTACCG 59.444 47.826 4.78 0.00 0.00 4.02
3696 15803 2.992543 TCAACAGCAACAGCAACAAAAC 59.007 40.909 0.00 0.00 0.00 2.43
3697 15804 2.008752 ACAGCAACAGCAACAAAACC 57.991 45.000 0.00 0.00 0.00 3.27
3730 15837 5.290493 TCCCTCGTTATCTTAATGCATGT 57.710 39.130 0.00 0.00 0.00 3.21
3749 15856 5.411361 GCATGTACAAAGTTGGATGTGTAGA 59.589 40.000 0.00 0.00 0.00 2.59
3756 15863 1.195442 TTGGATGTGTAGACGGGGCA 61.195 55.000 0.00 0.00 0.00 5.36
3940 16048 3.627123 TGCCTGAAACATGGATTATCGTG 59.373 43.478 0.00 0.00 0.00 4.35
3941 16049 3.627577 GCCTGAAACATGGATTATCGTGT 59.372 43.478 0.00 0.00 38.40 4.49
3942 16050 4.814234 GCCTGAAACATGGATTATCGTGTA 59.186 41.667 0.00 0.00 36.01 2.90
3943 16051 5.277345 GCCTGAAACATGGATTATCGTGTAC 60.277 44.000 0.00 0.00 36.01 2.90
3944 16052 6.049149 CCTGAAACATGGATTATCGTGTACT 58.951 40.000 0.00 0.00 36.01 2.73
3945 16053 7.207383 CCTGAAACATGGATTATCGTGTACTA 58.793 38.462 0.00 0.00 36.01 1.82
3946 16054 7.872993 CCTGAAACATGGATTATCGTGTACTAT 59.127 37.037 0.00 0.00 36.01 2.12
3947 16055 8.812147 TGAAACATGGATTATCGTGTACTATC 57.188 34.615 0.00 0.00 36.01 2.08
3948 16056 8.638873 TGAAACATGGATTATCGTGTACTATCT 58.361 33.333 0.00 0.00 36.01 1.98
3949 16057 9.130312 GAAACATGGATTATCGTGTACTATCTC 57.870 37.037 0.00 0.00 36.01 2.75
3950 16058 8.410673 AACATGGATTATCGTGTACTATCTCT 57.589 34.615 0.00 0.00 36.01 3.10
3951 16059 7.821652 ACATGGATTATCGTGTACTATCTCTG 58.178 38.462 0.00 0.00 35.36 3.35
3952 16060 7.448777 ACATGGATTATCGTGTACTATCTCTGT 59.551 37.037 0.00 0.00 35.36 3.41
3953 16061 8.947115 CATGGATTATCGTGTACTATCTCTGTA 58.053 37.037 0.00 0.00 0.00 2.74
3954 16062 8.913487 TGGATTATCGTGTACTATCTCTGTAA 57.087 34.615 0.00 0.00 0.00 2.41
3955 16063 9.346005 TGGATTATCGTGTACTATCTCTGTAAA 57.654 33.333 0.00 0.00 0.00 2.01
3956 16064 9.828852 GGATTATCGTGTACTATCTCTGTAAAG 57.171 37.037 0.00 0.00 0.00 1.85
3972 16080 9.871238 TCTCTGTAAAGAAATATAAGAGCGTTT 57.129 29.630 0.00 0.00 0.00 3.60
3989 16097 8.635877 AGAGCGTTTAGATCATTAAAGTAGTG 57.364 34.615 0.00 0.00 37.82 2.74
3990 16098 8.467598 AGAGCGTTTAGATCATTAAAGTAGTGA 58.532 33.333 0.00 0.00 37.82 3.41
3991 16099 9.250624 GAGCGTTTAGATCATTAAAGTAGTGAT 57.749 33.333 0.00 0.00 37.77 3.06
3992 16100 9.250624 AGCGTTTAGATCATTAAAGTAGTGATC 57.749 33.333 10.99 10.99 46.33 2.92
4019 16127 7.619964 AACACTTATATTTGTTTACGGAGGG 57.380 36.000 0.00 0.00 31.78 4.30
4020 16128 6.949715 ACACTTATATTTGTTTACGGAGGGA 58.050 36.000 0.00 0.00 0.00 4.20
4031 16139 5.246656 TGTTTACGGAGGGAGTAATTCTTGA 59.753 40.000 0.00 0.00 34.50 3.02
4213 16321 8.928270 AAAGTTAAACATAGTCGAGTGGATAG 57.072 34.615 2.10 0.00 0.00 2.08
4216 16324 8.189460 AGTTAAACATAGTCGAGTGGATAGTTC 58.811 37.037 2.10 0.00 0.00 3.01
4249 16357 5.991328 AGATGTACAAAGTCTTGTGTGTG 57.009 39.130 0.00 0.00 45.53 3.82
4278 16386 3.058224 GTGCCGAAGAAAAGTTATGCACT 60.058 43.478 0.00 0.00 43.25 4.40
4279 16387 3.058293 TGCCGAAGAAAAGTTATGCACTG 60.058 43.478 0.00 0.00 35.12 3.66
4280 16388 3.188460 GCCGAAGAAAAGTTATGCACTGA 59.812 43.478 0.00 0.00 35.12 3.41
4281 16389 4.320202 GCCGAAGAAAAGTTATGCACTGAA 60.320 41.667 0.00 0.00 35.12 3.02
4282 16390 5.385617 CCGAAGAAAAGTTATGCACTGAAG 58.614 41.667 0.00 0.00 35.12 3.02
4283 16391 5.049405 CCGAAGAAAAGTTATGCACTGAAGT 60.049 40.000 0.00 0.00 35.12 3.01
4284 16392 6.430451 CGAAGAAAAGTTATGCACTGAAGTT 58.570 36.000 0.00 0.00 35.12 2.66
4285 16393 6.912591 CGAAGAAAAGTTATGCACTGAAGTTT 59.087 34.615 0.00 0.00 35.12 2.66
4286 16394 8.067784 CGAAGAAAAGTTATGCACTGAAGTTTA 58.932 33.333 9.76 0.00 35.12 2.01
4287 16395 9.730420 GAAGAAAAGTTATGCACTGAAGTTTAA 57.270 29.630 9.76 0.00 35.12 1.52
4293 16401 9.816354 AAGTTATGCACTGAAGTTTAAATTTGT 57.184 25.926 0.00 0.00 35.12 2.83
4299 16407 9.672086 TGCACTGAAGTTTAAATTTGTATACAC 57.328 29.630 4.68 0.00 0.00 2.90
4300 16408 9.672086 GCACTGAAGTTTAAATTTGTATACACA 57.328 29.630 4.68 0.00 0.00 3.72
4302 16410 9.893305 ACTGAAGTTTAAATTTGTATACACAGC 57.107 29.630 4.68 0.00 35.67 4.40
4303 16411 9.891828 CTGAAGTTTAAATTTGTATACACAGCA 57.108 29.630 4.68 0.00 35.67 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.083164 TATGAAGAACATGCTGCAACACAG 60.083 41.667 6.36 0.00 43.38 3.66
8 9 2.022934 TGAAGAACATGCTGCAACACA 58.977 42.857 6.36 0.00 0.00 3.72
9 10 2.780065 TGAAGAACATGCTGCAACAC 57.220 45.000 6.36 0.00 0.00 3.32
10 11 4.074259 ACTATGAAGAACATGCTGCAACA 58.926 39.130 6.36 0.00 39.77 3.33
11 12 4.154737 TCACTATGAAGAACATGCTGCAAC 59.845 41.667 6.36 0.00 39.77 4.17
12 13 4.325972 TCACTATGAAGAACATGCTGCAA 58.674 39.130 6.36 0.00 39.77 4.08
13 14 3.941573 TCACTATGAAGAACATGCTGCA 58.058 40.909 4.13 4.13 39.77 4.41
14 15 4.952262 TTCACTATGAAGAACATGCTGC 57.048 40.909 0.00 0.00 39.77 5.25
15 16 5.277202 CGGATTCACTATGAAGAACATGCTG 60.277 44.000 0.00 0.00 40.05 4.41
16 17 4.813161 CGGATTCACTATGAAGAACATGCT 59.187 41.667 0.00 0.00 40.05 3.79
17 18 4.024556 CCGGATTCACTATGAAGAACATGC 60.025 45.833 0.00 0.00 40.05 4.06
18 19 5.007039 CACCGGATTCACTATGAAGAACATG 59.993 44.000 9.46 0.00 40.05 3.21
19 20 5.118990 CACCGGATTCACTATGAAGAACAT 58.881 41.667 9.46 0.00 40.05 2.71
20 21 4.503910 CACCGGATTCACTATGAAGAACA 58.496 43.478 9.46 0.00 40.05 3.18
21 22 3.309954 GCACCGGATTCACTATGAAGAAC 59.690 47.826 9.46 0.00 40.05 3.01
22 23 3.197766 AGCACCGGATTCACTATGAAGAA 59.802 43.478 9.46 0.00 40.05 2.52
23 24 2.766263 AGCACCGGATTCACTATGAAGA 59.234 45.455 9.46 0.00 40.05 2.87
24 25 2.868583 CAGCACCGGATTCACTATGAAG 59.131 50.000 9.46 0.00 40.05 3.02
25 26 2.236146 ACAGCACCGGATTCACTATGAA 59.764 45.455 9.46 0.00 41.09 2.57
26 27 1.831106 ACAGCACCGGATTCACTATGA 59.169 47.619 9.46 0.00 0.00 2.15
27 28 1.935873 CACAGCACCGGATTCACTATG 59.064 52.381 9.46 0.00 0.00 2.23
28 29 1.134401 CCACAGCACCGGATTCACTAT 60.134 52.381 9.46 0.00 0.00 2.12
29 30 0.249120 CCACAGCACCGGATTCACTA 59.751 55.000 9.46 0.00 0.00 2.74
30 31 1.003355 CCACAGCACCGGATTCACT 60.003 57.895 9.46 0.00 0.00 3.41
31 32 0.605319 TTCCACAGCACCGGATTCAC 60.605 55.000 9.46 0.00 0.00 3.18
32 33 0.327924 ATTCCACAGCACCGGATTCA 59.672 50.000 9.46 0.00 0.00 2.57
33 34 2.325583 TATTCCACAGCACCGGATTC 57.674 50.000 9.46 0.00 0.00 2.52
34 35 3.297134 AATATTCCACAGCACCGGATT 57.703 42.857 9.46 0.00 0.00 3.01
35 36 4.326826 CATAATATTCCACAGCACCGGAT 58.673 43.478 9.46 0.00 0.00 4.18
36 37 3.738982 CATAATATTCCACAGCACCGGA 58.261 45.455 9.46 0.00 0.00 5.14
37 38 2.226437 GCATAATATTCCACAGCACCGG 59.774 50.000 0.00 0.00 0.00 5.28
38 39 3.141398 AGCATAATATTCCACAGCACCG 58.859 45.455 0.00 0.00 0.00 4.94
39 40 4.794003 GCAAGCATAATATTCCACAGCACC 60.794 45.833 0.00 0.00 0.00 5.01
40 41 4.202040 TGCAAGCATAATATTCCACAGCAC 60.202 41.667 0.00 0.00 0.00 4.40
41 42 3.952967 TGCAAGCATAATATTCCACAGCA 59.047 39.130 0.00 0.00 0.00 4.41
42 43 4.572985 TGCAAGCATAATATTCCACAGC 57.427 40.909 0.00 0.00 0.00 4.40
43 44 8.971321 GTTTTATGCAAGCATAATATTCCACAG 58.029 33.333 23.50 0.00 44.99 3.66
44 45 8.473219 TGTTTTATGCAAGCATAATATTCCACA 58.527 29.630 23.50 16.61 44.99 4.17
45 46 8.870160 TGTTTTATGCAAGCATAATATTCCAC 57.130 30.769 23.50 14.90 44.99 4.02
46 47 9.695526 GATGTTTTATGCAAGCATAATATTCCA 57.304 29.630 23.50 15.03 44.99 3.53
47 48 9.695526 TGATGTTTTATGCAAGCATAATATTCC 57.304 29.630 23.50 14.99 44.99 3.01
55 56 8.238631 GGAAAAATTGATGTTTTATGCAAGCAT 58.761 29.630 12.66 12.66 38.92 3.79
56 57 7.308469 GGGAAAAATTGATGTTTTATGCAAGCA 60.308 33.333 0.00 0.00 31.43 3.91
57 58 7.022979 GGGAAAAATTGATGTTTTATGCAAGC 58.977 34.615 0.00 0.00 31.43 4.01
58 59 7.095271 ACGGGAAAAATTGATGTTTTATGCAAG 60.095 33.333 0.00 0.00 31.43 4.01
59 60 6.708054 ACGGGAAAAATTGATGTTTTATGCAA 59.292 30.769 0.00 0.00 31.43 4.08
60 61 6.226787 ACGGGAAAAATTGATGTTTTATGCA 58.773 32.000 0.00 0.00 31.43 3.96
61 62 6.720012 ACGGGAAAAATTGATGTTTTATGC 57.280 33.333 0.00 0.00 31.43 3.14
62 63 7.014702 GCAACGGGAAAAATTGATGTTTTATG 58.985 34.615 0.00 0.00 31.43 1.90
63 64 6.708054 TGCAACGGGAAAAATTGATGTTTTAT 59.292 30.769 0.00 0.00 31.43 1.40
64 65 6.049149 TGCAACGGGAAAAATTGATGTTTTA 58.951 32.000 0.00 0.00 31.43 1.52
65 66 4.878397 TGCAACGGGAAAAATTGATGTTTT 59.122 33.333 0.00 0.00 32.94 2.43
66 67 4.446371 TGCAACGGGAAAAATTGATGTTT 58.554 34.783 0.00 0.00 0.00 2.83
67 68 4.065321 TGCAACGGGAAAAATTGATGTT 57.935 36.364 0.00 0.00 0.00 2.71
68 69 3.742433 TGCAACGGGAAAAATTGATGT 57.258 38.095 0.00 0.00 0.00 3.06
69 70 4.388189 GTTGCAACGGGAAAAATTGATG 57.612 40.909 14.90 0.00 0.00 3.07
83 84 2.265073 ATATGCCCGTGCGTTGCAAC 62.265 55.000 19.89 19.89 41.47 4.17
84 85 2.043405 ATATGCCCGTGCGTTGCAA 61.043 52.632 0.00 0.00 41.47 4.08
85 86 2.437537 ATATGCCCGTGCGTTGCA 60.438 55.556 8.11 8.11 41.78 4.08
86 87 2.024588 CATATGCCCGTGCGTTGC 59.975 61.111 0.00 0.00 41.78 4.17
87 88 1.062365 CACATATGCCCGTGCGTTG 59.938 57.895 1.58 0.00 41.78 4.10
88 89 3.496711 CACATATGCCCGTGCGTT 58.503 55.556 1.58 0.00 41.78 4.84
94 95 7.898365 TTGATATATCACTAGCACATATGCCCG 60.898 40.741 15.10 0.00 44.29 6.13
95 96 7.275183 TTGATATATCACTAGCACATATGCCC 58.725 38.462 15.10 0.00 44.29 5.36
96 97 8.771766 CATTGATATATCACTAGCACATATGCC 58.228 37.037 15.10 0.00 44.29 4.40
97 98 8.771766 CCATTGATATATCACTAGCACATATGC 58.228 37.037 15.10 0.00 43.87 3.14
101 102 9.797642 TTTTCCATTGATATATCACTAGCACAT 57.202 29.630 15.10 1.72 36.36 3.21
102 103 9.797642 ATTTTCCATTGATATATCACTAGCACA 57.202 29.630 15.10 0.00 36.36 4.57
104 105 9.234827 CCATTTTCCATTGATATATCACTAGCA 57.765 33.333 15.10 0.67 36.36 3.49
105 106 8.186821 GCCATTTTCCATTGATATATCACTAGC 58.813 37.037 15.10 3.75 36.36 3.42
106 107 9.234827 TGCCATTTTCCATTGATATATCACTAG 57.765 33.333 15.10 3.68 36.36 2.57
107 108 9.585369 TTGCCATTTTCCATTGATATATCACTA 57.415 29.630 15.10 2.19 36.36 2.74
108 109 8.481492 TTGCCATTTTCCATTGATATATCACT 57.519 30.769 15.10 7.34 36.36 3.41
109 110 9.199982 CTTTGCCATTTTCCATTGATATATCAC 57.800 33.333 15.10 0.35 36.36 3.06
141 144 1.707427 AGCCTGTCCTGTTTTCTGGAT 59.293 47.619 0.00 0.00 46.70 3.41
159 162 2.612212 TGGCGGATCTAAAAATTCGAGC 59.388 45.455 0.00 0.00 28.52 5.03
188 194 9.797473 GTGTTCAGAACTTTTTCTTTTCAAAAG 57.203 29.630 14.51 3.20 40.34 2.27
238 247 2.173519 CCAACATTGTCCATTCTGCCT 58.826 47.619 0.00 0.00 0.00 4.75
239 248 1.205417 CCCAACATTGTCCATTCTGCC 59.795 52.381 0.00 0.00 0.00 4.85
240 249 1.404583 GCCCAACATTGTCCATTCTGC 60.405 52.381 0.00 0.00 0.00 4.26
241 250 1.894466 TGCCCAACATTGTCCATTCTG 59.106 47.619 0.00 0.00 0.00 3.02
261 270 4.111967 CCAGGTTCGGCCCAATTT 57.888 55.556 0.00 0.00 38.26 1.82
291 300 3.057736 CCGAAGAGAGGAACGAGTGTTTA 60.058 47.826 0.00 0.00 38.78 2.01
525 555 1.095600 GACAAGAAGGAAATCGGGGC 58.904 55.000 0.00 0.00 0.00 5.80
603 633 2.677037 GCCATTACAGCAAGTAGTCGGT 60.677 50.000 0.00 0.00 33.43 4.69
605 635 1.588404 CGCCATTACAGCAAGTAGTCG 59.412 52.381 0.00 0.00 33.43 4.18
662 692 1.152881 GGCGCCTCAATCCCTCAAT 60.153 57.895 22.15 0.00 0.00 2.57
706 736 3.057806 GTGAACCCACGGTTAAATCCAAG 60.058 47.826 0.00 0.00 46.95 3.61
759 838 1.056700 ATACCCGCATCTCCAGGCTT 61.057 55.000 0.00 0.00 0.00 4.35
770 849 2.614983 GCTCCGAAATTAAATACCCGCA 59.385 45.455 0.00 0.00 0.00 5.69
774 853 8.926715 AAATTTCTGCTCCGAAATTAAATACC 57.073 30.769 16.55 0.00 46.99 2.73
817 904 1.624813 CCAACCAATGTGCCAAGGAAT 59.375 47.619 0.00 0.00 0.00 3.01
878 977 7.231317 AGTTTTATGTGCAAAGAAAGAGGATGA 59.769 33.333 0.00 0.00 0.00 2.92
882 981 9.696917 AAATAGTTTTATGTGCAAAGAAAGAGG 57.303 29.630 0.00 0.00 0.00 3.69
994 1102 6.833041 TGGTTTCTTCAGTAACCATAGTGAA 58.167 36.000 12.65 6.10 46.10 3.18
1040 1148 1.000274 GGCGGTTTATGATGCATTCCC 60.000 52.381 0.00 0.00 0.00 3.97
1062 1170 0.824759 GCTCAATGAGGTCTACCGGT 59.175 55.000 13.98 13.98 42.08 5.28
1217 1325 0.821711 TGAAACCAAACCTCGCAGGG 60.822 55.000 7.06 0.00 40.58 4.45
1220 1328 1.452145 GCCTGAAACCAAACCTCGCA 61.452 55.000 0.00 0.00 0.00 5.10
1285 1393 1.688197 TGGCACTGCATATCTCGATGA 59.312 47.619 2.82 0.00 0.00 2.92
1482 1595 8.564574 TGTGTAATCTTGTATTCTTTTGTCACC 58.435 33.333 0.00 0.00 0.00 4.02
1534 1647 2.752238 TTTATTGTGGGGGCGGCG 60.752 61.111 0.51 0.51 0.00 6.46
1535 1648 1.379309 TCTTTATTGTGGGGGCGGC 60.379 57.895 0.00 0.00 0.00 6.53
1536 1649 0.322997 TGTCTTTATTGTGGGGGCGG 60.323 55.000 0.00 0.00 0.00 6.13
1606 1719 2.930826 AGAGCTTTTGGAGTTCGGAA 57.069 45.000 0.00 0.00 40.24 4.30
1710 1823 5.559770 TCAAAGGACATAACTGAATGCTGA 58.440 37.500 0.00 0.00 0.00 4.26
1778 1891 9.902684 GAGGACCATAATAATCATGATCTTCAT 57.097 33.333 9.06 0.00 37.65 2.57
1836 1949 6.483307 TGGTTTGAGCAGTTACTATGCATATC 59.517 38.462 6.92 0.00 46.31 1.63
1860 1973 3.869832 CAGTTCTGGCATCATAGTGACTG 59.130 47.826 0.00 0.00 0.00 3.51
1865 1978 4.833478 AGAACAGTTCTGGCATCATAGT 57.167 40.909 15.41 0.00 38.91 2.12
1866 1979 4.334759 CCAAGAACAGTTCTGGCATCATAG 59.665 45.833 16.85 0.00 40.59 2.23
1882 1995 1.736681 GATCTGCAGCTCACCAAGAAC 59.263 52.381 12.62 0.00 0.00 3.01
1922 2035 0.595095 GCTCCACCTTTGTTGCTCTG 59.405 55.000 0.00 0.00 0.00 3.35
1943 2059 5.182570 GGTGGGTTCTTAATGTTGTACTTCC 59.817 44.000 0.00 0.00 0.00 3.46
1968 2084 7.453126 ACAAAATGTGGACCCAGAATGTAATTA 59.547 33.333 0.00 0.00 36.07 1.40
2026 2142 5.121221 TCATACGAACATACATCATCGCT 57.879 39.130 0.00 0.00 38.80 4.93
2029 2145 6.422100 AGCAACTCATACGAACATACATCATC 59.578 38.462 0.00 0.00 0.00 2.92
2032 7589 6.589830 AAGCAACTCATACGAACATACATC 57.410 37.500 0.00 0.00 0.00 3.06
2068 7625 5.713389 TCACCATCTTGCTCAAATCAATCTT 59.287 36.000 0.00 0.00 0.00 2.40
2082 14178 6.149973 TGAAATCTAACAGCTTCACCATCTTG 59.850 38.462 0.00 0.00 0.00 3.02
2119 14218 4.534168 CAGTTGTGAGATTGCAAGTTCTG 58.466 43.478 7.29 2.91 0.00 3.02
2121 14220 3.303406 GCAGTTGTGAGATTGCAAGTTC 58.697 45.455 4.94 5.66 36.59 3.01
2148 14247 9.355215 CTGAATACTTCTAAACGTACAAGTGAT 57.645 33.333 10.15 1.88 31.52 3.06
2302 14401 6.655078 AGATTTCAGCCAACATACAGTTTT 57.345 33.333 0.00 0.00 38.74 2.43
2497 14596 3.067320 GGAATTACCTGATCTGCAAAGGC 59.933 47.826 0.00 0.00 34.18 4.35
2498 14597 4.907879 GGAATTACCTGATCTGCAAAGG 57.092 45.455 0.00 3.50 37.11 3.11
2580 14679 5.048921 CACACAATGTCTTTGCTCTTCAGAT 60.049 40.000 0.00 0.00 39.03 2.90
2632 14731 1.059098 TGGTTGCTGGAGTCTCATGT 58.941 50.000 1.47 0.00 0.00 3.21
2664 14763 1.745489 GCTCCACCCAGTTAAGCCG 60.745 63.158 0.00 0.00 0.00 5.52
2806 14905 6.759272 TGTAGTCAAGTCAACTTTATGAGCT 58.241 36.000 0.00 0.00 33.11 4.09
2835 14934 1.328986 GCTTTCAATCGCCTGAGTAGC 59.671 52.381 6.86 6.86 31.76 3.58
2856 14955 5.398603 ACTCTTCCGATCATATCATGGAC 57.601 43.478 0.00 0.00 0.00 4.02
2859 14958 7.147976 TGTGTAACTCTTCCGATCATATCATG 58.852 38.462 0.00 0.00 38.04 3.07
2913 15012 8.740207 CTAGCAAGCTAGAGCGGAAAGTTAAAA 61.740 40.741 21.49 0.00 46.56 1.52
2914 15013 7.339620 CTAGCAAGCTAGAGCGGAAAGTTAAA 61.340 42.308 21.49 0.00 46.56 1.52
2915 15014 5.907586 CTAGCAAGCTAGAGCGGAAAGTTAA 60.908 44.000 21.49 0.00 46.56 2.01
2916 15015 4.440250 CTAGCAAGCTAGAGCGGAAAGTTA 60.440 45.833 21.49 0.00 46.56 2.24
2917 15016 3.677424 CTAGCAAGCTAGAGCGGAAAGTT 60.677 47.826 21.49 0.00 46.56 2.66
2918 15017 2.159170 CTAGCAAGCTAGAGCGGAAAGT 60.159 50.000 21.49 0.00 46.56 2.66
2944 15043 8.822805 AGGAAACTAGAATTGATACAGGTAACA 58.177 33.333 0.00 0.00 40.61 2.41
3046 15145 8.783093 GCACATAACTGTAGCATAATGGAAATA 58.217 33.333 0.00 0.00 33.14 1.40
3054 15153 8.499403 TGTAAATGCACATAACTGTAGCATAA 57.501 30.769 12.59 5.67 43.23 1.90
3126 15225 6.162777 GGCAACTAATCAAATAAAGCACCAA 58.837 36.000 0.00 0.00 0.00 3.67
3166 15265 6.894339 TCCCCATTAGAAAAGAAAACACTC 57.106 37.500 0.00 0.00 0.00 3.51
3171 15270 8.398743 ACCTAGAATCCCCATTAGAAAAGAAAA 58.601 33.333 0.00 0.00 0.00 2.29
3205 15304 9.846248 GAAACATAAGCAAGAGTCAAATACAAT 57.154 29.630 0.00 0.00 0.00 2.71
3206 15305 8.845227 TGAAACATAAGCAAGAGTCAAATACAA 58.155 29.630 0.00 0.00 0.00 2.41
3216 15322 4.153117 ACGCTTCTGAAACATAAGCAAGAG 59.847 41.667 17.24 7.40 41.53 2.85
3217 15323 4.065088 ACGCTTCTGAAACATAAGCAAGA 58.935 39.130 17.24 0.00 41.53 3.02
3262 15368 2.880268 CCACTGTGATTCTGTGAAGCAA 59.120 45.455 9.86 0.00 44.93 3.91
3283 15389 2.027024 TATCACCATCGCCGTCGC 59.973 61.111 0.00 0.00 35.26 5.19
3290 15396 1.538204 CCCAAGTCCGTATCACCATCG 60.538 57.143 0.00 0.00 0.00 3.84
3294 15400 1.192428 AGTCCCAAGTCCGTATCACC 58.808 55.000 0.00 0.00 0.00 4.02
3295 15401 3.329929 AAAGTCCCAAGTCCGTATCAC 57.670 47.619 0.00 0.00 0.00 3.06
3296 15402 4.346730 TCTAAAGTCCCAAGTCCGTATCA 58.653 43.478 0.00 0.00 0.00 2.15
3297 15403 4.737055 GCTCTAAAGTCCCAAGTCCGTATC 60.737 50.000 0.00 0.00 0.00 2.24
3298 15404 3.132467 GCTCTAAAGTCCCAAGTCCGTAT 59.868 47.826 0.00 0.00 0.00 3.06
3299 15405 2.494870 GCTCTAAAGTCCCAAGTCCGTA 59.505 50.000 0.00 0.00 0.00 4.02
3447 15554 4.160252 GGTTGGGATGCTCAAACATAACAT 59.840 41.667 0.00 0.00 32.49 2.71
3466 15573 2.942376 TCATAGCGGCAATAGTTGGTTG 59.058 45.455 1.45 0.00 0.00 3.77
3517 15624 2.179018 CAAGGGATTTGCACCGCG 59.821 61.111 0.00 0.00 0.00 6.46
3530 15637 9.507329 AAGCTTATATATAATCCACACACAAGG 57.493 33.333 0.00 0.00 0.00 3.61
3605 15712 3.324556 AGAAGCTCTGAACTTGCTCTCTT 59.675 43.478 0.00 0.00 35.85 2.85
3606 15713 2.899256 AGAAGCTCTGAACTTGCTCTCT 59.101 45.455 0.00 0.00 35.85 3.10
3607 15714 3.317603 AGAAGCTCTGAACTTGCTCTC 57.682 47.619 0.00 0.00 35.85 3.20
3628 15735 5.349824 GACAGTTTGTCAGTTCAGGATTC 57.650 43.478 4.42 0.00 46.22 2.52
3654 15761 4.704540 TGAAATTCGGTACTTGAATGCCAT 59.295 37.500 12.53 3.33 36.24 4.40
3664 15771 3.880490 TGTTGCTGTTGAAATTCGGTACT 59.120 39.130 0.00 0.00 0.00 2.73
3670 15777 3.864583 TGTTGCTGTTGCTGTTGAAATTC 59.135 39.130 0.00 0.00 40.48 2.17
3696 15803 2.124942 GAGGGAGCAAGGAAGCGG 60.125 66.667 0.00 0.00 40.15 5.52
3697 15804 2.510238 CGAGGGAGCAAGGAAGCG 60.510 66.667 0.00 0.00 40.15 4.68
3730 15837 4.561938 CCCGTCTACACATCCAACTTTGTA 60.562 45.833 0.00 0.00 0.00 2.41
3763 15870 3.797353 GATGGAGCGAGGGGCCAA 61.797 66.667 4.39 0.00 45.17 4.52
3804 15911 0.532862 CAGAACACAAGGACGCCAGT 60.533 55.000 0.00 0.00 0.00 4.00
3946 16054 9.871238 AAACGCTCTTATATTTCTTTACAGAGA 57.129 29.630 0.00 0.00 0.00 3.10
3963 16071 9.088512 CACTACTTTAATGATCTAAACGCTCTT 57.911 33.333 0.00 0.00 0.00 2.85
3964 16072 8.467598 TCACTACTTTAATGATCTAAACGCTCT 58.532 33.333 0.00 0.00 0.00 4.09
3965 16073 8.630278 TCACTACTTTAATGATCTAAACGCTC 57.370 34.615 0.00 0.00 0.00 5.03
3966 16074 9.250624 GATCACTACTTTAATGATCTAAACGCT 57.749 33.333 8.21 0.00 43.55 5.07
3993 16101 9.165035 CCCTCCGTAAACAAATATAAGTGTTTA 57.835 33.333 15.31 15.31 44.13 2.01
3994 16102 7.884354 TCCCTCCGTAAACAAATATAAGTGTTT 59.116 33.333 16.76 16.76 46.73 2.83
3995 16103 7.396418 TCCCTCCGTAAACAAATATAAGTGTT 58.604 34.615 0.00 0.00 39.63 3.32
3996 16104 6.949715 TCCCTCCGTAAACAAATATAAGTGT 58.050 36.000 0.00 0.00 0.00 3.55
3997 16105 7.046033 ACTCCCTCCGTAAACAAATATAAGTG 58.954 38.462 0.00 0.00 0.00 3.16
3998 16106 7.191593 ACTCCCTCCGTAAACAAATATAAGT 57.808 36.000 0.00 0.00 0.00 2.24
3999 16107 9.774413 ATTACTCCCTCCGTAAACAAATATAAG 57.226 33.333 0.00 0.00 31.36 1.73
4001 16109 9.768662 GAATTACTCCCTCCGTAAACAAATATA 57.231 33.333 0.00 0.00 31.36 0.86
4002 16110 8.491958 AGAATTACTCCCTCCGTAAACAAATAT 58.508 33.333 0.00 0.00 31.36 1.28
4003 16111 7.854337 AGAATTACTCCCTCCGTAAACAAATA 58.146 34.615 0.00 0.00 31.36 1.40
4004 16112 6.718294 AGAATTACTCCCTCCGTAAACAAAT 58.282 36.000 0.00 0.00 31.36 2.32
4005 16113 6.117975 AGAATTACTCCCTCCGTAAACAAA 57.882 37.500 0.00 0.00 31.36 2.83
4006 16114 5.750352 AGAATTACTCCCTCCGTAAACAA 57.250 39.130 0.00 0.00 31.36 2.83
4007 16115 5.246656 TCAAGAATTACTCCCTCCGTAAACA 59.753 40.000 0.00 0.00 31.36 2.83
4008 16116 5.727434 TCAAGAATTACTCCCTCCGTAAAC 58.273 41.667 0.00 0.00 31.36 2.01
4009 16117 6.346096 CATCAAGAATTACTCCCTCCGTAAA 58.654 40.000 0.00 0.00 31.36 2.01
4010 16118 5.163343 CCATCAAGAATTACTCCCTCCGTAA 60.163 44.000 0.00 0.00 0.00 3.18
4011 16119 4.344102 CCATCAAGAATTACTCCCTCCGTA 59.656 45.833 0.00 0.00 0.00 4.02
4012 16120 3.134804 CCATCAAGAATTACTCCCTCCGT 59.865 47.826 0.00 0.00 0.00 4.69
4013 16121 3.388024 TCCATCAAGAATTACTCCCTCCG 59.612 47.826 0.00 0.00 0.00 4.63
4014 16122 5.373812 TTCCATCAAGAATTACTCCCTCC 57.626 43.478 0.00 0.00 0.00 4.30
4015 16123 6.836242 AGATTCCATCAAGAATTACTCCCTC 58.164 40.000 0.00 0.00 36.60 4.30
4016 16124 6.838401 AGATTCCATCAAGAATTACTCCCT 57.162 37.500 0.00 0.00 36.60 4.20
4017 16125 8.980481 TTAAGATTCCATCAAGAATTACTCCC 57.020 34.615 0.00 0.00 36.60 4.30
4018 16126 8.563732 GCTTAAGATTCCATCAAGAATTACTCC 58.436 37.037 6.67 0.00 36.60 3.85
4019 16127 9.113838 TGCTTAAGATTCCATCAAGAATTACTC 57.886 33.333 6.67 0.00 36.60 2.59
4020 16128 9.466497 TTGCTTAAGATTCCATCAAGAATTACT 57.534 29.630 6.67 0.00 36.60 2.24
4031 16139 2.654863 CCCGGTTGCTTAAGATTCCAT 58.345 47.619 6.67 0.00 0.00 3.41
4081 16189 3.498397 ACTGAACGAACAAAGGCATACTG 59.502 43.478 0.00 0.00 0.00 2.74
4084 16192 3.734463 TGACTGAACGAACAAAGGCATA 58.266 40.909 0.00 0.00 0.00 3.14
4092 16200 2.547855 CCACTCCATGACTGAACGAACA 60.548 50.000 0.00 0.00 0.00 3.18
4213 16321 9.274206 ACTTTGTACATCTTAAAGAAGGAGAAC 57.726 33.333 10.48 0.00 35.82 3.01
4216 16324 9.495572 AAGACTTTGTACATCTTAAAGAAGGAG 57.504 33.333 8.17 0.00 35.82 3.69
4249 16357 2.814336 ACTTTTCTTCGGCACCTTGATC 59.186 45.455 0.00 0.00 0.00 2.92


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.